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Chen D, Gu X, Nurzat Y, Xu L, Li X, Wu L, Jiao H, Gao P, Zhu X, Yan D, Li S, Xue C. Writers, readers, and erasers RNA modifications and drug resistance in cancer. Mol Cancer 2024; 23:178. [PMID: 39215288 PMCID: PMC11363509 DOI: 10.1186/s12943-024-02089-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
Drug resistance in cancer cells significantly diminishes treatment efficacy, leading to recurrence and metastasis. A critical factor contributing to this resistance is the epigenetic alteration of gene expression via RNA modifications, such as N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), 7-methylguanosine (m7G), pseudouridine (Ψ), and adenosine-to-inosine (A-to-I) editing. These modifications are pivotal in regulating RNA splicing, translation, transport, degradation, and stability. Governed by "writers," "readers," and "erasers," RNA modifications impact numerous biological processes and cancer progression, including cell proliferation, stemness, autophagy, invasion, and apoptosis. Aberrant RNA modifications can lead to drug resistance and adverse outcomes in various cancers. Thus, targeting RNA modification regulators offers a promising strategy for overcoming drug resistance and enhancing treatment efficacy. This review consolidates recent research on the role of prevalent RNA modifications in cancer drug resistance, with a focus on m6A, m1A, m5C, m7G, Ψ, and A-to-I editing. Additionally, it examines the regulatory mechanisms of RNA modifications linked to drug resistance in cancer and underscores the existing limitations in this field.
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Affiliation(s)
- Di Chen
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Xinyu Gu
- Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China
| | - Yeltai Nurzat
- State Key Laboratory of Respiratory Disease, Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lixia Xu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Xueyuan Li
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Lixin Wu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Henan Jiao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Peng Gao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Xuqiang Zhu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China.
| | - Dongming Yan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China.
| | - Shaohua Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China.
| | - Chen Xue
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China.
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Lenk R, Kleindienst W, Szabó GT, Baiersdörfer M, Boros G, Keller JM, Mahiny AJ, Vlatkovic I. Understanding the impact of in vitro transcription byproducts and contaminants. Front Mol Biosci 2024; 11:1426129. [PMID: 39050733 PMCID: PMC11266732 DOI: 10.3389/fmolb.2024.1426129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/14/2024] [Indexed: 07/27/2024] Open
Abstract
The success of messenger (m)RNA-based vaccines against SARS-CoV-2 during the COVID-19 pandemic has led to rapid growth and innovation in the field of mRNA-based therapeutics. However, mRNA production, whether in small amounts for research or large-scale GMP-grade for biopharmaceutics, is still based on the In Vitro Transcription (IVT) reaction developed in the early 1980s. The IVT reaction exploits phage RNA polymerase to catalyze the formation of an engineered mRNA that depends on a linearized DNA template, nucleotide building blocks, as well as pH, temperature, and reaction time. But depending on the IVT conditions and subsequent purification steps, diverse byproducts such as dsRNA, abortive RNAs and RNA:DNA hybrids might form. Unwanted byproducts, if not removed, could be formulated together with the full-length mRNA and cause an immune response in cells by activating host pattern recognition receptors. In this review, we summarize the potential types of IVT byproducts, their known biological activity, and how they can impact the efficacy and safety of mRNA therapeutics. In addition, we briefly overview non-nucleotide-based contaminants such as RNases, endotoxin and metal ions that, when present in the IVT reaction, can also influence the activity of mRNA-based drugs. We further discuss current approaches aimed at adjusting the IVT reaction conditions or improving mRNA purification to achieve optimal performance for medical applications.
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3
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Ding M, Xu W, Pei G, Li P. Long way up: rethink diseases in light of phase separation and phase transition. Protein Cell 2024; 15:475-492. [PMID: 38069453 PMCID: PMC11214837 DOI: 10.1093/procel/pwad057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/24/2023] [Indexed: 07/02/2024] Open
Abstract
Biomolecular condensation, driven by multivalency, serves as a fundamental mechanism within cells, facilitating the formation of distinct compartments, including membraneless organelles that play essential roles in various cellular processes. Perturbations in the delicate equilibrium of condensation, whether resulting in gain or loss of phase separation, have robustly been associated with cellular dysfunction and physiological disorders. As ongoing research endeavors wholeheartedly embrace this newly acknowledged principle, a transformative shift is occurring in our comprehension of disease. Consequently, significant strides have been made in unraveling the profound relevance and potential causal connections between abnormal phase separation and various diseases. This comprehensive review presents compelling recent evidence that highlight the intricate associations between aberrant phase separation and neurodegenerative diseases, cancers, and infectious diseases. Additionally, we provide a succinct summary of current efforts and propose innovative solutions for the development of potential therapeutics to combat the pathological consequences attributed to aberrant phase separation.
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Affiliation(s)
- Mingrui Ding
- State Key Laboratory of Membrane Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- NuPhase Therapeutics, Beijing 100083, China
| | - Weifan Xu
- State Key Laboratory of Membrane Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- NuPhase Therapeutics, Beijing 100083, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Pilong Li
- State Key Laboratory of Membrane Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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4
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Watkins JM, Burke JM. A closer look at mammalian antiviral condensates. Biochem Soc Trans 2024; 52:1393-1404. [PMID: 38778761 PMCID: PMC11234502 DOI: 10.1042/bst20231296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/01/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Several biomolecular condensates assemble in mammalian cells in response to viral infection. The most studied of these are stress granules (SGs), which have been proposed to promote antiviral innate immune signaling pathways, including the RLR-MAVS, the protein kinase R (PKR), and the OAS-RNase L pathways. However, recent studies have demonstrated that SGs either negatively regulate or do not impact antiviral signaling. Instead, the SG-nucleating protein, G3BP1, may function to perturb viral RNA biology by condensing viral RNA into viral-aggregated RNA condensates, thus explaining why viruses often antagonize G3BP1 or hijack its RNA condensing function. However, a recently identified condensate, termed double-stranded RNA-induced foci, promotes the activation of the PKR and OAS-RNase L antiviral pathways. In addition, SG-like condensates known as an RNase L-induced bodies (RLBs) have been observed during many viral infections, including SARS-CoV-2 and several flaviviruses. RLBs may function in promoting decay of cellular and viral RNA, as well as promoting ribosome-associated signaling pathways. Herein, we review these recent advances in the field of antiviral biomolecular condensates, and we provide perspective on the role of canonical SGs and G3BP1 during the antiviral response.
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Affiliation(s)
- J. Monty Watkins
- Department of Molecular Medicine, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, U.S.A
- Department of Immunology and Microbiology, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, U.S.A
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, U.S.A
| | - James M. Burke
- Department of Molecular Medicine, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, U.S.A
- Department of Immunology and Microbiology, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, U.S.A
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Karasik A, Lorenzi HA, DePass AV, Guydosh NR. Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response. Cell Rep 2024; 43:114287. [PMID: 38823018 PMCID: PMC11251458 DOI: 10.1016/j.celrep.2024.114287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 04/05/2024] [Accepted: 05/13/2024] [Indexed: 06/03/2024] Open
Abstract
Viral infection triggers several double-stranded RNA (dsRNA) sensors that lead to changes in gene expression in the cell. One of these sensors activates an endonuclease, ribonuclease L (RNase L), that cleaves single-stranded RNA. However, how the resultant widespread RNA fragmentation affects gene expression is not fully understood. Here, we show that this fragmentation induces the ribotoxic stress response via ZAKα, potentially through stalled ribosomes and/or ribosome collisions. The p38 and JNK pathways that are activated as part of this response promote outcomes that inhibit the virus, such as programmed cell death. We also show that RNase L limits the translation of stress-responsive genes. Intriguingly, we found that the activity of the generic endonuclease, RNase A, recapitulates many of the same molecular phenotypes as activated RNase L, demonstrating how widespread RNA cleavage can evoke an antiviral program.
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Affiliation(s)
- Agnes Karasik
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hernan A Lorenzi
- TriLab Bioinformatics Group, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew V DePass
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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6
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Liu D, Yang J, Cristea IM. Liquid-liquid phase separation in innate immunity. Trends Immunol 2024; 45:454-469. [PMID: 38762334 PMCID: PMC11247960 DOI: 10.1016/j.it.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024]
Abstract
Intrinsic and innate immune responses are essential lines of defense in the body's constant surveillance of pathogens. The discovery of liquid-liquid phase separation (LLPS) as a key regulator of this primal response to infection brings an updated perspective to our understanding of cellular defense mechanisms. Here, we review the emerging multifaceted role of LLPS in diverse aspects of mammalian innate immunity, including DNA and RNA sensing and inflammasome activity. We discuss the intricate regulation of LLPS by post-translational modifications (PTMs), and the subversive tactics used by viruses to antagonize LLPS. This Review, therefore, underscores the significance of LLPS as a regulatory node that offers rapid and plastic control over host immune signaling, representing a promising target for future therapeutic strategies.
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Affiliation(s)
- Dawei Liu
- Department of Molecular Biology, Princeton University; Princeton, NJ 08544, USA
| | - Jinhang Yang
- Department of Molecular Biology, Princeton University; Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University; Princeton, NJ 08544, USA.
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7
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Cusic R, Burke JM. Condensation of RNase L promotes its rapid activation in response to viral infection in mammalian cells. Sci Signal 2024; 17:eadi9844. [PMID: 38771918 PMCID: PMC11391522 DOI: 10.1126/scisignal.adi9844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 05/03/2024] [Indexed: 05/23/2024]
Abstract
Oligoadenylate synthetase 3 (OAS3) and ribonuclease L (RNase L) are components of a pathway that combats viral infection in mammals. Upon detection of viral double-stranded RNA (dsRNA), OAS3 synthesizes 2'-5'-oligo(A), which activates the RNase domain of RNase L by promoting the homodimerization and oligomerization of RNase L monomers. Activated RNase L rapidly degrades all cellular mRNAs, shutting off several cellular processes. We sought to understand the molecular mechanisms underlying the rapid activation of RNase L in response to viral infection. Through superresolution microscopy and live-cell imaging, we showed that OAS3 and RNase L concentrated into higher-order cytoplasmic complexes known as dsRNA-induced foci (dRIF) in response to dsRNA or infection with dengue virus, Zika virus, or West Nile virus. The concentration of OAS3 and RNase L at dRIF corresponded with the activation of RNase L-mediated RNA decay. We showed that dimerized/oligomerized RNase L concentrated in a liquid-like shell surrounding a core OAS3-dRIF structure and dynamically exchanged with the cytosol. These data establish that the condensation of dsRNA, OAS3, and RNase L into dRIF is a molecular switch that promotes the rapid activation of RNase L upon detection of dsRNA in mammalian cells.
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Affiliation(s)
- Renee Cusic
- Department of Molecular Medicine, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, United States of America
- Department of Immunology and Microbiology, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, United States of America
| | - James M. Burke
- Department of Molecular Medicine, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, United States of America
- Department of Immunology and Microbiology, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, United States of America
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8
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Andreakos E. Type I and type III interferons: From basic biology and genetics to clinical development for COVID-19 and beyond. Semin Immunol 2024; 72:101863. [PMID: 38271892 DOI: 10.1016/j.smim.2024.101863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/11/2023] [Accepted: 01/02/2024] [Indexed: 01/27/2024]
Abstract
Type I and type III interferons (IFNs) constitute a key antiviral defense systems of the body, inducing viral resistance to cells and mediating diverse innate and adaptive immune functions. Defective type I and type III IFN responses have recently emerged as the 'Achilles heel' in COVID-19, with such patients developing severe disease and exhibiting a high risk for critical pneumonia and death. Here, we review the biology of type I and type III IFNs, their similarities and important functional differences, and their roles in SARS-CoV-2 infection. We also appraise the various mechanisms proposed to drive defective IFN responses in COVID-19 with particular emphasis to the ability of SARS-CoV-2 to suppress IFN production and activities, the genetic factors involved and the presence of autoantibodies neutralizing IFNs and accounting for a large proportion of individuals with severe COVID-19. Finally, we discuss the long history of the type I IFN therapeutics for the treatment of viral diseases, cancer and multiple sclerosis, the various efforts to use them in respiratory infections, and the newly emerging type III IFN therapeutics, with emphasis to the more recent studies on COVID-19 and their potential use as broad spectrum antivirals for future epidemics or pandemics.
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Affiliation(s)
- Evangelos Andreakos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, BRFAA, Athens, Greece.
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9
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Burke JM, Ratnayake OC, Watkins JM, Perera R, Parker R. G3BP1-dependent condensation of translationally inactive viral RNAs antagonizes infection. SCIENCE ADVANCES 2024; 10:eadk8152. [PMID: 38295168 PMCID: PMC10830107 DOI: 10.1126/sciadv.adk8152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024]
Abstract
G3BP1 is an RNA binding protein that condenses untranslating messenger RNAs into stress granules (SGs). G3BP1 is inactivated by multiple viruses and is thought to antagonize viral replication by SG-enhanced antiviral signaling. Here, we show that neither G3BP1 nor SGs generally alter the activation of innate immune pathways. Instead, we show that the RNAs encoded by West Nile virus, Zika virus, and severe acute respiratory syndrome coronavirus 2 are prone to G3BP1-dependent RNA condensation, which is enhanced by limiting translation initiation and correlates with the disruption of viral replication organelles and viral RNA replication. We show that these viruses counteract condensation of their RNA genomes by inhibiting the RNA condensing function of G3BP proteins, hijacking the RNA decondensing activity of eIF4A, and/or maintaining efficient translation. These findings argue that RNA condensation can function as an intrinsic antiviral mechanism, which explains why many viruses inactivate G3BP proteins and suggests that SGs may have arisen as a vestige of this antiviral mechanism.
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Affiliation(s)
- James M. Burke
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Oshani C. Ratnayake
- Center for Vector-Borne and Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
- Center for Metabolism of Infectious Diseases, Colorado State University, Fort Collins, CO 80523, USA
| | - J. Monty Watkins
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL 33438, USA
| | - Rushika Perera
- Center for Vector-Borne and Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
- Center for Metabolism of Infectious Diseases, Colorado State University, Fort Collins, CO 80523, USA
| | - Roy Parker
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
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10
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He S, Gou H, Zhou Y, Wu C, Ren X, Wu X, Guan G, Jin B, Huang J, Jin Z, Zhao T. The SARS-CoV-2 nucleocapsid protein suppresses innate immunity by remodeling stress granules to atypical foci. FASEB J 2023; 37:e23269. [PMID: 37889852 DOI: 10.1096/fj.202201973rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 08/10/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023]
Abstract
Viruses deploy multiple strategies to suppress the host innate immune response to facilitate viral replication and pathogenesis. Typical G3BP1+ stress granules (SGs) are usually formed in host cells after virus infection to restrain viral translation and to stimulate innate immunity. Thus, viruses have evolved various mechanisms to inhibit SGs or to repurpose SG components such as G3BP1. Previous studies showed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection inhibited host immunity during the early stage of COVID-19. However, the precise mechanism is not yet well understood. Here we showed that the SARS-CoV-2 nucleocapsid (SARS2-N) protein suppressed the double-stranded RNA (dsRNA)-induced innate immune response, concomitant with inhibition of SGs and the induction of atypical SARS2-N+ /G3BP1+ foci (N+ foci). The SARS2-N protein-induced formation of N+ foci was dependent on the ability of its ITFG motif to hijack G3BP1, which contributed to suppress the innate immune response. Importantly, SARS2-N protein facilitated viral replication by inducing the formation of N+ foci. Viral mutations within SARS2-N protein that impair the formation of N+ foci are associated with the inability of the SARS2-N protein to suppress the immune response. Taken together, our study has revealed a novel mechanism by which SARS-CoV-2 suppresses the innate immune response via induction of atypical N+ foci. We think that this is a critical strategy for viral pathogenesis and has potential therapeutic implications.
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Affiliation(s)
- Su He
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Hongwei Gou
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Yulin Zhou
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Chunxiu Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Xinxin Ren
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Xiajunpeng Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Guanwen Guan
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Boxing Jin
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Jinhua Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Zhigang Jin
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Tiejun Zhao
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
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11
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Chathuranga WAG, Nikapitiya C, Kim JH, Chathuranga K, Weerawardhana A, Dodantenna N, Kim DJ, Poo H, Jung JU, Lee CH, Lee JS. Gadd45β is critical for regulation of type I interferon signaling by facilitating G3BP-mediated stress granule formation. Cell Rep 2023; 42:113358. [PMID: 37917584 DOI: 10.1016/j.celrep.2023.113358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/04/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023] Open
Abstract
Stress granules (SGs) constitute a signaling hub that plays a critical role in type I interferon responses. Here, we report that growth arrest and DNA damage-inducible beta (Gadd45β) act as a positive regulator of SG-mediated interferon signaling by targeting G3BP upon RNA virus infection. Gadd45β deficiency markedly impairs SG formation and SG-mediated activation of interferon signaling in vitro. Gadd45β knockout mice are highly susceptible to RNA virus infection, and their ability to produce interferon and cytokines is severely impaired. Specifically, Gadd45β interacts with the RNA-binding domain of G3BP, leading to conformational expansion of G3BP1 via dissolution of its autoinhibitory electrostatic intramolecular interaction. The acidic loop 1- and RNA-binding properties of Gadd45β markedly increase the conformational expansion and RNA-binding affinity of the G3BP1-Gadd45β complex, thereby promoting assembly of SGs. These findings suggest a role for Gadd45β as a component and critical regulator of G3BP1-mediated SG formation, which facilitates RLR-mediated interferon signaling.
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Affiliation(s)
- W A Gayan Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Chamilani Nikapitiya
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Jae-Hoon Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea; Livestock Products Analysis Division, Division of Animal Health, Daejeon Metropolitan City Institute of Health and Environment, Daejeon 34146, Republic of Korea
| | - Kiramage Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Asela Weerawardhana
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Niranjan Dodantenna
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Doo-Jin Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Haryoung Poo
- Department of Biomedical Science and Engineering, Konkuk Institute of Technology, Konkuk University, Seoul 05029, Republic of Korea
| | - Jae U Jung
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRRIB), Daejeon 34141, Republic of Korea.
| | - Jong-Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea.
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12
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Ottens F, Efstathiou S, Hoppe T. Cutting through the stress: RNA decay pathways at the endoplasmic reticulum. Trends Cell Biol 2023:S0962-8924(23)00236-2. [PMID: 38008608 DOI: 10.1016/j.tcb.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/28/2023]
Abstract
The endoplasmic reticulum (ER) is central to the processing of luminal, transmembrane, and secretory proteins, and maintaining a functional ER is essential for organismal physiology and health. Increased protein-folding load on the ER causes ER stress, which activates quality control mechanisms to restore ER function and protein homeostasis. Beyond protein quality control, mRNA decay pathways have emerged as potent ER fidelity regulators, but their mechanistic roles in ER quality control and their interrelationships remain incompletely understood. Herein, we review ER-associated RNA decay pathways - including regulated inositol-requiring enzyme 1α (IRE1α)-dependent mRNA decay (RIDD), nonsense-mediated mRNA decay (NMD), and Argonaute-dependent RNA silencing - in ER homeostasis, and highlight the intricate coordination of ER-targeted RNA and protein decay mechanisms and their association with antiviral defense.
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Affiliation(s)
- Franziska Ottens
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sotirios Efstathiou
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, Cologne, Germany.
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13
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González Aparicio LJ, Yang Y, Hackbart M, López CB. Copy-back viral genomes induce a cellular stress response that interferes with viral protein expression without affecting antiviral immunity. PLoS Biol 2023; 21:e3002381. [PMID: 37983241 PMCID: PMC10695362 DOI: 10.1371/journal.pbio.3002381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/04/2023] [Accepted: 10/15/2023] [Indexed: 11/22/2023] Open
Abstract
Antiviral responses are often accompanied by translation inhibition and formation of stress granules (SGs) in infected cells. However, the triggers for these processes and their role during infection remain subjects of active investigation. Copy-back viral genomes (cbVGs) are the primary inducers of the mitochondrial antiviral signaling (MAVS) pathway and antiviral immunity during Sendai virus (SeV) and respiratory syncytial virus (RSV) infections. The relationship between cbVGs and cellular stress during viral infections is unknown. Here, we show that SGs form during infections containing high levels of cbVGs, and not during infections with low levels of cbVGs. Moreover, using RNA fluorescent in situ hybridization to differentiate accumulation of standard viral genomes from cbVGs at a single-cell level during infection, we show that SGs form exclusively in cells that accumulate high levels of cbVGs. Protein kinase R (PKR) activation is increased during high cbVG infections and, as expected, is necessary for virus-induced SGs. However, SGs form independent of MAVS signaling, demonstrating that cbVGs induce antiviral immunity and SG formation through 2 independent mechanisms. Furthermore, we show that translation inhibition and SG formation do not affect the overall expression of interferon and interferon stimulated genes during infection, making the stress response dispensable for global antiviral immunity. Using live-cell imaging, we show that SG formation is highly dynamic and correlates with a drastic reduction of viral protein expression even in cells infected for several days. Through analysis of active protein translation at a single-cell level, we show that infected cells that form SGs show inhibition of protein translation. Together, our data reveal a new cbVG-driven mechanism of viral interference where cbVGs induce PKR-mediated translation inhibition and SG formation, leading to a reduction in viral protein expression without altering overall antiviral immunity.
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Affiliation(s)
- Lavinia J. González Aparicio
- Department of Molecular Microbiology and Center for Women Infectious Disease Research, Washington University School of Medicine in St. Louis, Missouri, United States of America
| | - Yanling Yang
- Department of Molecular Microbiology and Center for Women Infectious Disease Research, Washington University School of Medicine in St. Louis, Missouri, United States of America
| | - Matthew Hackbart
- Department of Molecular Microbiology and Center for Women Infectious Disease Research, Washington University School of Medicine in St. Louis, Missouri, United States of America
| | - Carolina B. López
- Department of Molecular Microbiology and Center for Women Infectious Disease Research, Washington University School of Medicine in St. Louis, Missouri, United States of America
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14
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Sun H, Wu M, Zhang Z, Wang Y, Yang J, Liu Z, Guan G, Luo J, Yin H, Niu Q. OAS1 suppresses African swine fever virus replication by recruiting TRIM21 to degrade viral major capsid protein. J Virol 2023; 97:e0121723. [PMID: 37815352 PMCID: PMC10617512 DOI: 10.1128/jvi.01217-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/28/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE African swine fever virus (ASFV) completes the replication process by resisting host antiviral response via inhibiting interferon (IFN) secretion and interferon-stimulated genes (ISGs) function. 2', 5'-Oligoadenylate synthetase gene 1 (OAS1) has been reported to inhibit the replication of various RNA and some DNA viruses. However, the regulatory mechanisms involved in the ASFV-induced IFN-related pathway still need to be fully elucidated. Here, we found that OAS1, as a critical host factor, inhibits ASFV replication in an RNaseL-dependent manner. Furthermore, overexpression of OAS1 can promote the activation of the JAK-STAT pathway promoting innate immune responses. In addition, OAS1 plays a new function, which could interact with ASFV P72 protein to suppress ASFV infection. Mechanistically, OAS1 enhances the proteasomal degradation of P72 by promoting TRIM21-mediated ubiquitination. Meanwhile, P72 inhibits the production of avSG and affects the interaction between OAS1 and DDX6. Our findings demonstrated OAS1 as an important target against ASFV replication and revealed the mechanisms and intrinsic regulatory relationships during ASFV infection.
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Affiliation(s)
- Hualin Sun
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mengli Wu
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zhonghui Zhang
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yiwang Wang
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jifei Yang
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zhijie Liu
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Guiquan Guan
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianxun Luo
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hong Yin
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Qingli Niu
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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15
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Karasik A, Lorenzi HA, DePass AV, Guydosh NR. Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555507. [PMID: 37693516 PMCID: PMC10491309 DOI: 10.1101/2023.09.01.555507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Viral infection triggers several dsRNA sensors that lead to changes in gene expression in the cell. One of these sensors activates an endonuclease, RNase L, that cleaves single stranded RNA. However, how the resultant widespread RNA fragmentation affects gene expression is not fully understood. Here we show that this fragmentation induces the Ribotoxic Stress Response via ZAKα, potentially through ribosome collisions. The p38 and JNK pathways that are activated as part of this response promote outcomes that inhibit the virus, such as programmed cell death. We also show that RNase L limits the translation of stress-responsive genes, including antiviral IFIT mRNAs and GADD34 that encodes an antagonist of the Integrated Stress Response. Intriguingly, we found the activity of the generic endonuclease, RNase A, recapitulates many of the same molecular phenotypes as activated RNase L, demonstrating how widespread RNA cleavage can evoke an antiviral program.
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Affiliation(s)
- Agnes Karasik
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Hernan A Lorenzi
- TriLab Bioinformatics Group, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Andrew V DePass
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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16
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Lopez CB, Gonzalez Aparicio LJ, Yang Y, Hackbart MS. Copy-back viral genomes induce a cellular stress response that interferes with viral protein expression without affecting antiviral immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541157. [PMID: 37292625 PMCID: PMC10245731 DOI: 10.1101/2023.05.17.541157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Antiviral responses are often accompanied by translation inhibition and formation of stress granules (SG) in infected cells. However, the triggers for these processes and their role during infection remain subjects of active investigation. Copy-back viral genomes (cbVGs) are the primary inducers of the Mitochondrial Antiviral Signaling (MAVS) pathway and antiviral immunity during Sendai Virus (SeV) and Respiratory Syncytial virus (RSV) infections. The relationship between cbVGs and cellular stress during viral infections is unknown. Here we show that SG form during infections containing high levels of cbVGs, and not during infections with low levels of cbVGs. Moreover, using RNA fluorescent in situ hybridization to differentiate accumulation of standard viral genomes from cbVGs at a single-cell level during infection, we show that SG form exclusively in cells that accumulate high levels of cbVGs. PKR activation is increased during high cbVG infections and, as expected, PKR is necessary to induce virus-induced SG. However, SG form independent of MAVS signaling, demonstrating that cbVGs induce antiviral immunity and SG formation through two independent mechanisms. Furthermore, we show that translation inhibition and SG formation do not affect the overall expression of interferon and interferon stimulated genes during infection, making the stress response dispensable for antiviral immunity. Using live-cell imaging, we show that SG formation is highly dynamic and correlates with a drastic reduction of viral protein expression even in cells infected for several days. Through analysis of active protein translation at a single cell level, we show that infected cells that form SG show inhibition of protein translation. Together, our data reveal a new cbVG-driven mechanism of viral interference where cbVGs induce PKR-mediated translation inhibition and SG formation leading to a reduction in viral protein expression without altering overall antiviral immunity.
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17
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Baymiller M, Moon SL. Stress Granules as Causes and Consequences of Translation Suppression. Antioxid Redox Signal 2023; 39:390-409. [PMID: 37183403 PMCID: PMC10443205 DOI: 10.1089/ars.2022.0164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/05/2023] [Accepted: 05/01/2023] [Indexed: 05/16/2023]
Abstract
Significance: Stress granules (SGs) are biomolecular condensates that form upon global translation suppression during stress. SGs are enriched in translation factors and messenger RNAs (mRNAs), which they may sequester away from the protein synthesis machinery. While this is hypothesized to remodel the functional transcriptome during stress, it remains unclear whether SGs are a cause, or simply a consequence, of translation repression. Understanding the function of SGs is particularly important because they are implicated in numerous diseases including viral infections, cancer, and neurodegeneration. Recent Advances: We synthesize recent SG research spanning biological scales, from observing single proteins and mRNAs within one cell to measurements of the entire transcriptome or proteome of SGs in a cell population. We use the emerging understanding from these studies to suggest that SGs likely have less impact on global translation, but instead may strongly influence the translation of individual mRNAs localized to them. Critical Issues: Development of a unified model that links stress-induced RNA-protein condensation to regulation of downstream gene expression holds promise for understanding the mechanisms of cellular resilience. Future Directions: Therefore, upcoming research should clarify what influence SGs exert on translation at all scales as well as the molecular mechanisms that enable this. The resulting knowledge will be required to drive discovery in how SGs allow organisms to adapt to challenges and support health or go awry and lead to disease. Antioxid. Redox Signal. 39, 390-409.
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Affiliation(s)
- Max Baymiller
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephanie L. Moon
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
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18
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Li T, Li X, Wang X, Chen X, Zhao G, Liu C, Bao M, Song J, Li J, Huang L, Rong J, Tian K, Deng J, Zhu J, Cai X, Bu Z, Zheng J, Weng C. African swine fever virus pS273R antagonizes stress granule formation by cleaving the nucleating protein G3BP1 to facilitate viral replication. J Biol Chem 2023; 299:104844. [PMID: 37209818 PMCID: PMC10404608 DOI: 10.1016/j.jbc.2023.104844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 05/08/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
Cytoplasmic stress granules (SGs) are generally triggered by stress-induced translation arrest for storing mRNAs. Recently, it has been shown that SGs are regulated by different stimulators including viral infection, which is involved in the antiviral activity of host cells to limit viral propagation. To survive, several viruses have been reported to execute various strategies, such as modulating SG formation, to create optimal surroundings for viral replication. African swine fever virus (ASFV) is one of the most notorious pathogens in the global pig industry. However, the interplay between ASFV infection and SG formation remains largely unknown. In this study, we found that ASFV infection inhibited SG formation. Through SG inhibitory screening, we found that several ASFV-encoded proteins are involved in inhibition of SG formation. Among them, an ASFV S273R protein (pS273R), the only cysteine protease encoded by the ASFV genome, significantly affected SG formation. ASFV pS273R interacted with G3BP1 (Ras-GTPase-activating protein [SH3 domain] binding protein 1), a vital nucleating protein of SG formation. Furthermore, we found that ASFV pS273R cleaved G3BP1 at the G140-F141 to produce two fragments (G3BP1-N1-140 and G3BP1-C141-456). Interestingly, both the pS273R-cleaved fragments of G3BP1 lost the ability to induce SG formation and antiviral activity. Taken together, our finding reveals that the proteolytic cleavage of G3BP1 by ASFV pS273R is a novel mechanism by which ASFV counteracts host stress and innate antiviral responses.
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Affiliation(s)
- Tingting Li
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Xuewen Li
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China; College of Life Sciences, Yangtze University, Jingzhou, China
| | - Xiao Wang
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Xin Chen
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Gaihong Zhao
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Chuanxia Liu
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Miaofei Bao
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Jie Song
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Jiangnan Li
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Li Huang
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Jun Rong
- College of Life Sciences, Yangtze University, Jingzhou, China
| | - Kegong Tian
- National Research Center for Veterinary Medicine, Luoyang, China
| | - Junhua Deng
- Luoyang Putai Biotechnology Co, Ltd, Luoyang, China
| | - Jianzhong Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xuehui Cai
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhigao Bu
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jun Zheng
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China.
| | - Changjiang Weng
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China.
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19
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Burke JM. Regulation of ribonucleoprotein condensates by RNase L during viral infection. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1770. [PMID: 36479619 PMCID: PMC10244490 DOI: 10.1002/wrna.1770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/10/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
In response to viral infection, mammalian cells activate several innate immune pathways to antagonize viral gene expression. Upon recognition of viral double-stranded RNA, protein kinase R (PKR) phosphorylates the alpha subunit of eukaryotic initiation factor 2 (eIF2α) on serine 51. This inhibits canonical translation initiation, which broadly antagonizes viral protein synthesis. It also promotes the assembly of cytoplasmic ribonucleoprotein complexes termed stress granules (SGs). SGs are widely thought to promote cell survival and antiviral signaling. However, co-activation of the OAS/RNase L antiviral pathway inhibits the assembly of SGs and promotes the assembly of an alternative ribonucleoprotein complex termed an RNase L-dependent body (RLB). The formation of RLBs has been observed in response to double-stranded RNA, dengue virus infection, or SARS-CoV-2 infection. Herein, we review the distinct biogenesis pathways and properties of SGs and RLBs, and we provide perspective on their potential functions during the antiviral response. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Turnover and Surveillance > Regulation of RNA Stability RNA Export and Localization > RNA Localization.
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Affiliation(s)
- James M. Burke
- Department of Molecular Medicine, University of Florida Scripps Biomedical Research, Jupiter, Florida 33458, USA
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20
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Corbet GA, Burke JM, Parker R. Nucleic acid-protein condensates in innate immune signaling. EMBO J 2023; 42:e111870. [PMID: 36178199 PMCID: PMC10068312 DOI: 10.15252/embj.2022111870] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/24/2022] [Accepted: 09/19/2022] [Indexed: 11/09/2022] Open
Abstract
The presence of foreign nucleic acids in the cytosol is a marker of infection. Cells have sensors, also known as pattern recognition receptors (PRRs), in the cytosol that detect foreign nucleic acid and initiate an innate immune response. Recent studies have reported the condensation of multiple PRRs including PKR, NLRP6, and cGAS, with their nucleic acid activators into discrete nucleoprotein assemblies. Nucleic acid-protein condensates form due to multivalent interactions and can create high local concentrations of components. The formation of PRR-containing condensates may alter the magnitude or timing of PRR activation. In addition, unique condensates form following RNase L activation or during paracrine signaling from virally infected cells that may play roles in antiviral defense. These observations suggest that condensate formation may be a conserved mechanism that cells use to regulate activation of the innate immune response and open an avenue for further investigation into the composition and function of these condensates. Here we review the nucleic acid-protein granules that are implicated in the innate immune response, discuss general consequences of condensate formation and signal transduction, as well as what outstanding questions remain.
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Affiliation(s)
- Giulia A Corbet
- Department of BiochemistryUniversity of ColoradoBoulderCOUSA
| | - James M Burke
- Department of BiochemistryUniversity of ColoradoBoulderCOUSA
- Present address:
Department of Molecular MedicineUniversity of Florida Scripps Biomedical ResearchJupiterFLUSA
| | - Roy Parker
- Department of BiochemistryUniversity of ColoradoBoulderCOUSA
- Howard Hughes Medical InstituteChevy ChaseMDUSA
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21
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Ramnani B, Powell S, Shetty AG, Manivannan P, Hibbard BR, Leaman DW, Malathi K. Viral Hemorrhagic Septicemia Virus Activates Integrated Stress Response Pathway and Induces Stress Granules to Regulate Virus Replication. Viruses 2023; 15:466. [PMID: 36851680 PMCID: PMC9965902 DOI: 10.3390/v15020466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
Virus infection activates integrated stress response (ISR) and stress granule (SG) formation and viruses counteract by interfering with SG assembly, suggesting an important role in antiviral defense. The infection of fish cells by Viral Hemorrhagic Septicemia Virus (VHSV), activates the innate immune recognition pathway and the production of type I interferon (IFN). However, the mechanisms by which VHSV interacts with ISR pathway regulating SG formation is poorly understood. Here, we demonstrate that fish cells respond to heat shock, oxidative stress and VHSV infection by forming SG that localized key SG marker, Ras GTPase-activating protein (SH3 domain)-binding protein 1 (G3BP1). We show that PKR-like endoplasmic reticulum kinase (PERK), but not (dsRNA)-dependent protein kinase (PKR), is required for VHSV-induced SG formation. Furthermore, in VHSV Ia infected cells, PERK activity is required for IFN production, antiviral signaling and viral replication. SG formation required active virus replication as individual VHSV Ia proteins or inactive virus did not induce SG. Cells lacking G3BP1 produced increased IFN, antiviral genes and viral mRNA, however viral protein synthesis and viral titers were reduced. We show a critical role of the activation of ISR pathway and SG formation highlighting a novel role of G3BP1 in regulating VHSV protein translation and replication.
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Affiliation(s)
- Barkha Ramnani
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Shelby Powell
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Adarsh G. Shetty
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Praveen Manivannan
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Brian R. Hibbard
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Douglas W. Leaman
- College of Sciences, Auburn University at Montgomery, 7400 East Dr., Montgomery, AL 36117, USA
| | - Krishnamurthy Malathi
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
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22
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Dolliver SM, Kleer M, Bui-Marinos MP, Ying S, Corcoran JA, Khaperskyy DA. Nsp1 proteins of human coronaviruses HCoV-OC43 and SARS-CoV2 inhibit stress granule formation. PLoS Pathog 2022; 18:e1011041. [PMID: 36534661 PMCID: PMC9810206 DOI: 10.1371/journal.ppat.1011041] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/03/2023] [Accepted: 12/03/2022] [Indexed: 12/23/2022] Open
Abstract
Stress granules (SGs) are cytoplasmic condensates that often form as part of the cellular antiviral response. Despite the growing interest in understanding the interplay between SGs and other biological condensates and viral replication, the role of SG formation during coronavirus infection remains poorly understood. Several proteins from different coronaviruses have been shown to suppress SG formation upon overexpression, but there are only a handful of studies analyzing SG formation in coronavirus-infected cells. To better understand SG inhibition by coronaviruses, we analyzed SG formation during infection with the human common cold coronavirus OC43 (HCoV-OC43) and the pandemic SARS-CoV2. We did not observe SG induction in infected cells and both viruses inhibited eukaryotic translation initiation factor 2α (eIF2α) phosphorylation and SG formation induced by exogenous stress. Furthermore, in SARS-CoV2 infected cells we observed a sharp decrease in the levels of SG-nucleating protein G3BP1. Ectopic overexpression of nucleocapsid (N) and non-structural protein 1 (Nsp1) from both HCoV-OC43 and SARS-CoV2 inhibited SG formation. The Nsp1 proteins of both viruses inhibited arsenite-induced eIF2α phosphorylation, and the Nsp1 of SARS-CoV2 alone was sufficient to cause a decrease in G3BP1 levels. This phenotype was dependent on the depletion of cytoplasmic mRNA mediated by Nsp1 and associated with nuclear accumulation of the SG-nucleating protein TIAR. To test the role of G3BP1 in coronavirus replication, we infected cells overexpressing EGFP-tagged G3BP1 with HCoV-OC43 and observed a significant decrease in virus replication compared to control cells expressing EGFP. The antiviral role of G3BP1 and the existence of multiple SG suppression mechanisms that are conserved between HCoV-OC43 and SARS-CoV2 suggest that SG formation may represent an important antiviral host defense that coronaviruses target to ensure efficient replication.
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Affiliation(s)
- Stacia M. Dolliver
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Canada
| | - Mariel Kleer
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
- Snyder Institute for Chronic Diseases and Charbonneau Institute for Cancer Research, University of Calgary, Calgary, Canada
| | - Maxwell P. Bui-Marinos
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
- Snyder Institute for Chronic Diseases and Charbonneau Institute for Cancer Research, University of Calgary, Calgary, Canada
| | - Shan Ying
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Canada
| | - Jennifer A. Corcoran
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
- Snyder Institute for Chronic Diseases and Charbonneau Institute for Cancer Research, University of Calgary, Calgary, Canada
| | - Denys A. Khaperskyy
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Canada
- * E-mail:
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23
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Banerjee S, Smith C, Geballe AP, Rothenburg S, Kitzman JO, Brennan G. Gene amplification acts as a molecular foothold to facilitate cross-species adaptation and evasion of multiple antiviral pathways. Virus Evol 2022; 8:veac105. [PMID: 36483110 PMCID: PMC9724558 DOI: 10.1093/ve/veac105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/06/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Cross-species spillover events are responsible for many of the pandemics in human history including COVID-19; however, the evolutionary mechanisms that enable these events are poorly understood. We have previously modeled this process using a chimeric vaccinia virus expressing the rhesus cytomegalovirus-derived protein kinase R (PKR) antagonist RhTRS1 in place of its native PKR antagonists: E3L and K3L (VACVΔEΔK + RhTRS1). Using this virus, we demonstrated that gene amplification of rhtrs1 occurred early during experimental evolution and was sufficient to fully rescue virus replication in partially resistant African green monkey (AGM) fibroblasts. Notably, this rapid gene amplification also allowed limited virus replication in otherwise completely non-permissive human fibroblasts, suggesting that gene amplification may act as a 'molecular foothold' to facilitate viral adaptation to multiple species. In this study, we demonstrate that there are multiple barriers to VACVΔEΔK + RhTRS1 replication in human cells, mediated by both PKR and ribonuclease L (RNase L). We experimentally evolved three AGM-adapted virus populations in human fibroblasts. Each population adapted to human cells bimodally, via an initial 10-fold increase in replication after only two passages followed by a second 10-fold increase in replication by passage 9. Using our Illumina-based pipeline, we found that some single nucleotide polymorphisms (SNPs) which had evolved during the prior AGM adaptation were rapidly lost, while thirteen single-base substitutions and short indels increased over time, including two SNPs unique to human foreskin fibroblast (HFF)-adapted populations. Many of these changes were associated with components of the viral RNA polymerase, although no variant was shared between all three populations. Taken together, our results demonstrate that rhtrs1 amplification was sufficient to increase viral tropism after passage in an 'intermediate species' and subsequently enabled the virus to adopt different, species-specific adaptive mechanisms to overcome distinct barriers to viral replication in AGM and human cells.
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Affiliation(s)
- Shefali Banerjee
- †Current address for SB: Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Adam P Geballe
- Departments of Human Genetics and Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA,Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Jacob O Kitzman
- Departments of Microbiology and Medicine, University of Washington, Seattle, WA 98195, USA
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24
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Wang W, Pyle AM. The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands. Mol Cell 2022; 82:4131-4144.e6. [DOI: 10.1016/j.molcel.2022.09.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 08/09/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
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25
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Corbet GA, Burke JM, Bublitz GR, Tay JW, Parker R. dsRNA-induced condensation of antiviral proteins modulates PKR activity. Proc Natl Acad Sci U S A 2022; 119:e2204235119. [PMID: 35939694 PMCID: PMC9388085 DOI: 10.1073/pnas.2204235119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/01/2022] [Indexed: 12/21/2022] Open
Abstract
Mammalian cells respond to dsRNA in multiple manners. One key response to dsRNA is the activation of PKR, an eIF2α kinase, which triggers translational arrest and the formation of stress granules. However, the process of PKR activation in cells is not fully understood. In response to increased endogenous or exogenous dsRNA, we observed that PKR forms novel cytosolic condensates, referred to as dsRNA-induced foci (dRIFs). dRIFs contain dsRNA, form in proportion to dsRNA, and are enhanced by longer dsRNAs. dRIFs enrich several other dsRNA-binding proteins, including ADAR1, Stau1, NLRP1, and PACT. Strikingly, dRIFs correlate with and form before translation repression by PKR and localize to regions of cells where PKR activation is initiated. We hypothesize that dRIF formation is a mechanism that cells use to enhance the sensitivity of PKR activation in response to low levels of dsRNA or to overcome viral inhibitors of PKR activation.
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Affiliation(s)
- Giulia A. Corbet
- Department of Biochemistry, University of Colorado, Boulder, CO 80309
| | - James M. Burke
- Department of Biochemistry, University of Colorado, Boulder, CO 80309
| | - Gaia R. Bublitz
- Department of Biochemistry, University of Colorado, Boulder, CO 80309
| | | | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO 80309
- BioFrontiers Institute, Boulder, CO 80309
- Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789
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26
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Tejera-Hernández B, Goodman DE, Nevarez JM, Spindler KR. Mouse Adenovirus Type 1 E4orf6 Induces PKR Degradation. J Virol 2022; 96:e0206321. [PMID: 35285681 PMCID: PMC9006929 DOI: 10.1128/jvi.02063-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/12/2022] [Indexed: 11/20/2022] Open
Abstract
Protein kinase R (PKR) is a cellular kinase involved in the antiviral response. The inactivation or inhibition of this protein is a conserved activity in DNA and RNA virus infections. In contrast to human adenovirus type 5, mouse adenovirus type 1 (MAV-1) inhibits PKR activity through proteasome-dependent degradation. However, the molecular mechanism by which this process takes place is not fully understood. We investigated whether ubiquitination, MAV-1 early region 1B 55k (E1B 55k), and early region 4 orf6 (E4orf6) play a role in PKR degradation in MAV-1 infection, because the enzyme 3 (E3) ubiquitin ligase activity with these viral proteins is conserved among the Adenoviridae family. We provide evidence that E4orf6 is sufficient to induce mouse PKR degradation and that proteasome pathway inhibition blocks PKR degradation. Inhibition of neddylation of cullin, a component of E3 ubiquitin ligase complex, blocked efficient PKR degradation in MAV-1-infected cells. Finally, we demonstrated that MAV-1 degradation of PKR is specific for mouse PKR. These results indicate that counteracting PKR is mechanistically different in two species of adenoviruses. IMPORTANCE Viruses have evolved to counteract the immune system to successfully replicate in the host. Downregulation of several antiviral proteins is important for productive viral infection. Protein kinase R (PKR) is an antiviral protein that belongs to the first line of defense of the host. Because PKR senses dsRNA and blocks the cellular translation process during viral infections, it is not surprising that many viruses counteract this antiviral activity. We previously reported PKR degradation during mouse adenovirus type 1 (MAV-1) infection; however, the molecular mechanism of this activity was not fully known. This work provides evidence about the MAV-1 protein that induces PKR degradation and expands knowledge about involvement of the proteasome pathway.
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Affiliation(s)
- Berto Tejera-Hernández
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Danielle E. Goodman
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Juan M. Nevarez
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Katherine R. Spindler
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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27
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Chan CP, Jin DY. Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations. RNA (NEW YORK, N.Y.) 2022; 28:449-477. [PMID: 35031583 PMCID: PMC8925969 DOI: 10.1261/rna.079016.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Sensing of pathogen-associated molecular patterns including viral RNA by innate immunity represents the first line of defense against viral infection. In addition to RIG-I-like receptors and NOD-like receptors, several other RNA sensors are known to mediate innate antiviral response in the cytoplasm. Double-stranded RNA-binding protein PACT interacts with prototypic RNA sensor RIG-I to facilitate its recognition of viral RNA and induction of host interferon response, but variations of this theme are seen when the functions of RNA sensors are modulated by other RNA-binding proteins to impinge on antiviral defense, proinflammatory cytokine production and cell death programs. Their discrete and coordinated actions are crucial to protect the host from infection. In this review, we will focus on cytoplasmic RNA sensors with an emphasis on their interplay with RNA-binding partners. Classical sensors such as RIG-I will be briefly reviewed. More attention will be brought to new insights on how RNA-binding partners of RNA sensors modulate innate RNA sensing and how viruses perturb the functions of RNA-binding partners.
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Affiliation(s)
- Chi-Ping Chan
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
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28
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Chawla K, Subramanian G, Rahman T, Fan S, Chakravarty S, Gujja S, Demchak H, Chakravarti R, Chattopadhyay S. Autophagy in Virus Infection: A Race between Host Immune Response and Viral Antagonism. IMMUNO 2022; 2:153-169. [PMID: 35252965 PMCID: PMC8893043 DOI: 10.3390/immuno2010012] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Virus-infected cells trigger a robust innate immune response and facilitate virus replication. Here, we review the role of autophagy in virus infection, focusing on both pro-viral and anti-viral host responses using a select group of viruses. Autophagy is a cellular degradation pathway operated at the basal level to maintain homeostasis and is induced by external stimuli for specific functions. The degradative function of autophagy is considered a cellular anti-viral immune response. However, autophagy is a double-edged sword in viral infection; viruses often benefit from it, and the infected cells can also use it to inhibit viral replication. In addition to viral regulation, autophagy pathway proteins also function in autophagy-independent manners to regulate immune responses. Since viruses have co-evolved with hosts, they have developed ways to evade the anti-viral autophagic responses of the cells. Some of these mechanisms are also covered in our review. Lastly, we conclude with the thought that autophagy can be targeted for therapeutic interventions against viral diseases.
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Affiliation(s)
- Karan Chawla
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Gayatri Subramanian
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Tia Rahman
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Shumin Fan
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Sukanya Chakravarty
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Shreyas Gujja
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Hayley Demchak
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Ritu Chakravarti
- Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Saurabh Chattopadhyay
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
- Correspondence:
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29
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Iadevaia V, Burke JM, Eke L, Moller-Levet C, Parker R, Locker N. Novel stress granules-like structures are induced via a paracrine mechanism during viral infection. J Cell Sci 2022; 135:274514. [PMID: 35098996 PMCID: PMC8976915 DOI: 10.1242/jcs.259194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/13/2022] [Indexed: 11/20/2022] Open
Abstract
To rapidly adapt to stresses such as infections, cells have evolved several mechanisms, which include the activation of stress response pathways and the innate immune response. These stress responses result in the rapid inhibition of translation and condensation of stalled mRNAs with RNA-binding proteins and signalling components into cytoplasmic biocondensates called stress granules (SGs). Increasing evidence suggests that SGs contribute to antiviral defence and thus viruses need to evade these responses to propagate. We previously showed that Feline Calicivirus (FCV) impairs SGs assembly by cleaving the scaffolding protein G3BP1. We also observed that uninfected bystander cells assembled G3BP1-positive granules, suggesting a paracrine response triggered by infection. We now present evidence that virus-free supernatant generated from infected cells can induce the formation of SG-like foci, that we named paracrine granules. They are linked to antiviral activity and exhibit specific kinetics of assembly-disassembly, and protein and RNA composition that are different from canonical SGs. We propose that this paracrine induction reflects a novel cellular defence mechanism to limit viral propagation and promote stress responses in bystander cells.
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Affiliation(s)
- Valentina Iadevaia
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - James M. Burke
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Lucy Eke
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Carla Moller-Levet
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
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30
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Li J, Boix E. Host Defence RNases as Antiviral Agents against Enveloped Single Stranded RNA Viruses. Virulence 2021; 12:444-469. [PMID: 33660566 PMCID: PMC7939569 DOI: 10.1080/21505594.2021.1871823] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/26/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023] Open
Abstract
Owing to the recent outbreak of Coronavirus Disease of 2019 (COVID-19), it is urgent to develop effective and safe drugs to treat the present pandemic and prevent other viral infections that might come in the future. Proteins from our own innate immune system can serve as ideal sources of novel drug candidates thanks to their safety and immune regulation versatility. Some host defense RNases equipped with antiviral activity have been reported over time. Here, we try to summarize the currently available information on human RNases that can target viral pathogens, with special focus on enveloped single-stranded RNA (ssRNA) viruses. Overall, host RNases can fight viruses by a combined multifaceted strategy, including the enzymatic target of the viral genome, recognition of virus unique patterns, immune modulation, control of stress granule formation, and induction of autophagy/apoptosis pathways. The review also includes a detailed description of representative enveloped ssRNA viruses and their strategies to interact with the host and evade immune recognition. For comparative purposes, we also provide an exhaustive revision of the currently approved or experimental antiviral drugs. Finally, we sum up the current perspectives of drug development to achieve successful eradication of viral infections.
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Affiliation(s)
- Jiarui Li
- Dpt. Of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma De Barcelona, Spain
| | - Ester Boix
- Dpt. Of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma De Barcelona, Spain
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31
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Su X, Ma W, Feng D, Cheng B, Wang Q, Guo Z, Zhou D, Tang X. Efficient Inhibition of SARS‐CoV‐2 Using Chimeric Antisense Oligonucleotides through RNase L Activation**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaoxuan Su
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Wenxiao Ma
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Di Feng
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Boyang Cheng
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Zefeng Guo
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
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32
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Thoresen D, Wang W, Galls D, Guo R, Xu L, Pyle AM. The molecular mechanism of RIG-I activation and signaling. Immunol Rev 2021; 304:154-168. [PMID: 34514601 PMCID: PMC9293153 DOI: 10.1111/imr.13022] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 12/25/2022]
Abstract
RIG‐I is our first line of defense against RNA viruses, serving as a pattern recognition receptor that identifies molecular features common among dsRNA and ssRNA viral pathogens. RIG‐I is maintained in an inactive conformation as it samples the cellular space for pathogenic RNAs. Upon encounter with the triphosphorylated terminus of blunt‐ended viral RNA duplexes, the receptor changes conformation and releases a pair of signaling domains (CARDs) that are selectively modified and interact with an adapter protein (MAVS), thereby triggering a signaling cascade that stimulates transcription of interferons. Here, we describe the structural determinants for specific RIG‐I activation by viral RNA, and we describe the strategies by which RIG‐I remains inactivated in the presence of host RNAs. From the initial RNA triggering event to the final stages of interferon expression, we describe the experimental evidence underpinning our working knowledge of RIG‐I signaling. We draw parallels with behavior of related proteins MDA5 and LGP2, describing evolutionary implications of their collective surveillance of the cell. We conclude by describing the cell biology and immunological investigations that will be needed to accurately describe the role of RIG‐I in innate immunity and to provide the necessary foundation for pharmacological manipulation of this important receptor.
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Affiliation(s)
- Daniel Thoresen
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Wenshuai Wang
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Drew Galls
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Rong Guo
- Chemistry, Yale University, New Haven, CT, USA
| | - Ling Xu
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Anna Marie Pyle
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Chemistry, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
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33
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Su X, Ma W, Feng D, Cheng B, Wang Q, Guo Z, Zhou D, Tang X. Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation*. Angew Chem Int Ed Engl 2021; 60:21662-21667. [PMID: 34278671 PMCID: PMC8426974 DOI: 10.1002/anie.202105942] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Indexed: 12/14/2022]
Abstract
There is an urgent need to develop antiviral drugs and alleviate the current COVID-19 pandemic. Herein we report the design and construction of chimeric oligonucleotides comprising a 2'-OMe-modified antisense oligonucleotide and a 5'-phosphorylated 2'-5' poly(A)4 (4A2-5 ) to degrade envelope and spike RNAs of SARS-CoV-2. The oligonucleotide was used for searching and recognizing target viral RNA sequence, and the conjugated 4A2-5 was used for guided RNase L activation to sequence-specifically degrade viral RNAs. Since RNase L can potently cleave single-stranded RNA during innate antiviral response, degradation efficiencies with these chimeras were twice as much as those with only antisense oligonucleotides for both SARS-CoV-2 RNA targets. In pseudovirus infection models, chimera-S4 achieved potent and broad-spectrum inhibition of SARS-CoV-2 and its N501Y and/or ΔH69/ΔV70 mutants, indicating a promising antiviral agent based on the nucleic acid-hydrolysis targeting chimera (NATAC) strategy.
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Affiliation(s)
- Xiaoxuan Su
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Wenxiao Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Di Feng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Boyang Cheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Zefeng Guo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
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34
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Karasik A, Jones GD, DePass AV, Guydosh NR. Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences. Nucleic Acids Res 2021; 49:6007-6026. [PMID: 33556964 DOI: 10.1093/nar/gkab036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/06/2021] [Accepted: 02/03/2021] [Indexed: 11/15/2022] Open
Abstract
Ribonuclease L (RNase L) is activated as part of the innate immune response and plays an important role in the clearance of viral infections. When activated, it endonucleolytically cleaves both viral and host RNAs, leading to a global reduction in protein synthesis. However, it remains unknown how widespread RNA decay, and consequent changes in the translatome, promote the elimination of viruses. To study how this altered transcriptome is translated, we assayed the global distribution of ribosomes in RNase L activated human cells with ribosome profiling. We found that RNase L activation leads to a substantial increase in the fraction of translating ribosomes in ORFs internal to coding sequences (iORFs) and ORFs within 5' and 3' UTRs (uORFs and dORFs). Translation of these alternative ORFs was dependent on RNase L's cleavage activity, suggesting that mRNA decay fragments are translated to produce short peptides that may be important for antiviral activity.
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Affiliation(s)
- Agnes Karasik
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grant D Jones
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew V DePass
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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35
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Yu H, Bruneau RC, Brennan G, Rothenburg S. Battle Royale: Innate Recognition of Poxviruses and Viral Immune Evasion. Biomedicines 2021; 9:biomedicines9070765. [PMID: 34356829 PMCID: PMC8301327 DOI: 10.3390/biomedicines9070765] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 12/17/2022] Open
Abstract
Host pattern recognition receptors (PRRs) sense pathogen-associated molecular patterns (PAMPs), which are molecular signatures shared by different pathogens. Recognition of PAMPs by PRRs initiate innate immune responses via diverse signaling pathways. Over recent decades, advances in our knowledge of innate immune sensing have enhanced our understanding of the host immune response to poxviruses. Multiple PRR families have been implicated in poxvirus detection, mediating the initiation of signaling cascades, activation of transcription factors, and, ultimately, the expression of antiviral effectors. To counteract the host immune defense, poxviruses have evolved a variety of immunomodulators that have diverse strategies to disrupt or circumvent host antiviral responses triggered by PRRs. These interactions influence the outcomes of poxvirus infections. This review focuses on our current knowledge of the roles of PRRs in the recognition of poxviruses, their elicited antiviral effector functions, and how poxviral immunomodulators antagonize PRR-mediated host immune responses.
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36
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Markiewicz L, Drazkowska K, Sikorski PJ. Tricks and threats of RNA viruses - towards understanding the fate of viral RNA. RNA Biol 2021; 18:669-687. [PMID: 33618611 PMCID: PMC8078519 DOI: 10.1080/15476286.2021.1875680] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/22/2020] [Accepted: 01/09/2021] [Indexed: 12/24/2022] Open
Abstract
Human innate cellular defence pathways have evolved to sense and eliminate pathogens, of which, viruses are considered one of the most dangerous. Their relatively simple structure makes the identification of viral invasion a difficult task for cells. In the course of evolution, viral nucleic acids have become one of the strongest and most reliable early identifiers of infection. When considering RNA virus recognition, RNA sensing is the central mechanism in human innate immunity, and effectiveness of this sensing is crucial for triggering an appropriate antiviral response. Although human cells are armed with a variety of highly specialized receptors designed to respond only to pathogenic viral RNA, RNA viruses have developed an array of mechanisms to avoid being recognized by human interferon-mediated cellular defence systems. The repertoire of viral evasion strategies is extremely wide, ranging from masking pathogenic RNA through end modification, to utilizing sophisticated techniques to deceive host cellular RNA degrading enzymes, and hijacking the most basic metabolic pathways in host cells. In this review, we aim to dissect human RNA sensing mechanisms crucial for antiviral immune defences, as well as the strategies adopted by RNA viruses to avoid detection and degradation by host cells. We believe that understanding the fate of viral RNA upon infection, and detailing the molecular mechanisms behind virus-host interactions, may be helpful for developing more effective antiviral strategies; which are urgently needed to prevent the far-reaching consequences of widespread, highly pathogenic viral infections.
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37
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Mateju D, Chao JA. Stress granules: regulators or by-products? FEBS J 2021; 289:363-373. [PMID: 33725420 DOI: 10.1111/febs.15821] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/07/2021] [Accepted: 03/12/2021] [Indexed: 12/13/2022]
Abstract
Cells have to deal with conditions that can cause damage to biomolecules and eventually cell death. To protect against these adverse conditions and promote recovery, cells undergo dramatic changes upon exposure to stress. This involves activation of signaling pathways, cell cycle arrest, translational reprogramming, and reorganization of the cytoplasm. Notably, many stress conditions cause a global inhibition of mRNA translation accompanied by the formation of cytoplasmic condensates called stress granules (SGs), which sequester mRNA together with RNA-binding proteins, translation initiation factors, and other components. SGs are highly conserved in eukaryotes, suggesting that they perform an important function during the stress response. Over the years, many different roles have been assigned to SGs, including translational control, mRNA storage, regulation of mRNA decay, antiviral innate immune response, and modulation of signaling pathways. Most of our understanding, however, has been deduced from correlative data based upon the composition of SGs and only recently have technological innovations allowed hypotheses for SG function to be directly tested. Here, we discuss these challenges and explore the evidence related to the function of SGs.
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Affiliation(s)
- Daniel Mateju
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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38
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Wang HT, Hur S. Substrate recognition by TRIM and TRIM-like proteins in innate immunity. Semin Cell Dev Biol 2021; 111:76-85. [PMID: 33092958 PMCID: PMC7572318 DOI: 10.1016/j.semcdb.2020.09.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 09/28/2020] [Indexed: 12/23/2022]
Abstract
TRIM (Tripartite motif) and TRIM-like proteins have emerged as an important class of E3 ligases in innate immunity. Their functions range from activation or regulation of innate immune signaling pathway to direct detection and restriction of pathogens. Despite the importance, molecular mechanisms for many TRIM/TRIM-like proteins remain poorly characterized, in part due to challenges of identifying their substrates. In this review, we discuss several TRIM/TRIM-like proteins in RNA sensing pathways and viral restriction functions. We focus on those containing PRY-SPRY, the domain most frequently used for substrate recognition, and discuss emerging mechanisms that are commonly utilized by several TRIM/TRIM-like proteins to tightly control their interaction with the substrates.
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Affiliation(s)
- Hai-Tao Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
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39
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Ramnani B, Manivannan P, Jaggernauth S, Malathi K. ABCE1 Regulates RNase L-Induced Autophagy during Viral Infections. Viruses 2021; 13:v13020315. [PMID: 33670646 PMCID: PMC7922175 DOI: 10.3390/v13020315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 12/15/2022] Open
Abstract
Host response to a viral infection includes the production of type I interferon (IFN) and the induction of interferon-stimulated genes that have broad antiviral effects. One of the key antiviral effectors is the IFN-inducible oligoadenylate synthetase/ribonuclease L (OAS/RNase L) pathway, which is activated by double-stranded RNA to synthesize unique oligoadenylates, 2-5A, to activate RNase L. RNase L exerts an antiviral effect by cleaving diverse RNA substrates, limiting viral replication; many viruses have evolved mechanisms to counteract the OAS/RNase L pathway. Here, we show that the ATP-binding cassette E1 (ABCE1) transporter, identified as an inhibitor of RNase L, regulates RNase L activity and RNase L-induced autophagy during viral infections. ABCE1 knockdown cells show increased RNase L activity when activated by 2-5A. Compared to parental cells, the autophagy-inducing activity of RNase L in ABCE1-depleted cells is enhanced with early onset. RNase L activation in ABCE1-depleted cells inhibits cellular proliferation and sensitizes cells to apoptosis. Increased activity of caspase-3 causes premature cleavage of autophagy protein, Beclin-1, promoting a switch from autophagy to apoptosis. ABCE1 regulates autophagy during EMCV infection, and enhanced autophagy in ABCE1 knockdown cells promotes EMCV replication. We identify ABCE1 as a host protein that inhibits the OAS/RNase L pathway by regulating RNase L activity, potentially affecting antiviral effects.
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The Paradoxes of Viral mRNA Translation during Mammalian Orthoreovirus Infection. Viruses 2021; 13:v13020275. [PMID: 33670092 PMCID: PMC7916891 DOI: 10.3390/v13020275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
De novo viral protein synthesis following entry into host cells is essential for viral replication. As a consequence, viruses have evolved mechanisms to engage the host translational machinery while at the same time avoiding or counteracting host defenses that act to repress translation. Mammalian orthoreoviruses are dsRNA-containing viruses whose mRNAs were used as models for early investigations into the mechanisms that underpin the recognition and engagement of eukaryotic mRNAs by host cell ribosomes. However, there remain many unanswered questions and paradoxes regarding translation of reoviral mRNAs in the context of infection. This review summarizes the current state of knowledge about reovirus translation, identifies key unanswered questions, and proposes possible pathways toward a better understanding of reovirus translation.
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Eiermann N, Haneke K, Sun Z, Stoecklin G, Ruggieri A. Dance with the Devil: Stress Granules and Signaling in Antiviral Responses. Viruses 2020; 12:v12090984. [PMID: 32899736 PMCID: PMC7552005 DOI: 10.3390/v12090984] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
Cells have evolved highly specialized sentinels that detect viral infection and elicit an antiviral response. Among these, the stress-sensing protein kinase R, which is activated by double-stranded RNA, mediates suppression of the host translation machinery as a strategy to limit viral replication. Non-translating mRNAs rapidly condensate by phase separation into cytosolic stress granules, together with numerous RNA-binding proteins and components of signal transduction pathways. Growing evidence suggests that the integrated stress response, and stress granules in particular, contribute to antiviral defense. This review summarizes the current understanding of how stress and innate immune signaling act in concert to mount an effective response against virus infection, with a particular focus on the potential role of stress granules in the coordination of antiviral signaling cascades.
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Affiliation(s)
- Nina Eiermann
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Katharina Haneke
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Zhaozhi Sun
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany;
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany;
- Correspondence:
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Cascarina SM, Ross ED. A proposed role for the SARS-CoV-2 nucleocapsid protein in the formation and regulation of biomolecular condensates. FASEB J 2020; 34:9832-9842. [PMID: 32562316 PMCID: PMC7323129 DOI: 10.1096/fj.202001351] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 05/31/2020] [Indexed: 02/06/2023]
Abstract
To date, the recently discovered SARS-CoV-2 virus has afflicted >6.9 million people worldwide and disrupted the global economy. Development of effective vaccines or treatments for SARS-CoV-2 infection will be aided by a molecular-level understanding of SARS-CoV-2 proteins and their interactions with host cell proteins. The SARS-CoV-2 nucleocapsid (N) protein is highly homologous to the N protein of SARS-CoV, which is essential for viral RNA replication and packaging into new virions. Emerging models indicate that nucleocapsid proteins of other viruses can form biomolecular condensates to spatiotemporally regulate N protein localization and function. Our bioinformatic analyses, in combination with pre-existing experimental evidence, suggest that the SARS-CoV-2 N protein is capable of forming or regulating biomolecular condensates in vivo by interaction with RNA and key host cell proteins. We discuss multiple models, whereby the N protein of SARS-CoV-2 may harness this activity to regulate viral life cycle and host cell response to viral infection.
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Affiliation(s)
- Sean M. Cascarina
- Department of Biochemistry and Molecular BiologyColorado State UniversityFort CollinsCOUSA
| | - Eric D. Ross
- Department of Biochemistry and Molecular BiologyColorado State UniversityFort CollinsCOUSA
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Infectious Bronchitis Virus Regulates Cellular Stress Granule Signaling. Viruses 2020; 12:v12050536. [PMID: 32422883 PMCID: PMC7291021 DOI: 10.3390/v12050536] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 12/21/2022] Open
Abstract
Viruses must hijack cellular translation machinery to express viral genes. In many cases, this is impeded by cellular stress responses. These stress responses result in the global inhibition of translation and the storage of stalled mRNAs, into RNA-protein aggregates called stress granules. This results in the translational silencing of the majority of mRNAs excluding those beneficial for the cell to resolve the specific stress. For example, the expression of antiviral factors is maintained during viral infection. Here we investigated stress granule regulation by Gammacoronavirus infectious bronchitis virus (IBV), which causes the economically important poultry disease, infectious bronchitis. Interestingly, we found that IBV is able to inhibit multiple cellular stress granule signaling pathways, whilst at the same time, IBV replication also results in the induction of seemingly canonical stress granules in a proportion of infected cells. Moreover, IBV infection uncouples translational repression and stress granule formation and both processes are independent of eIF2α phosphorylation. These results provide novel insights into how IBV modulates cellular translation and antiviral stress signaling.
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